Digital Commons Network^™

Efficient Preservation Of Old Methane-Derived Organic Carbon In Deep-Sea Surface Sediments, Rui Bao, Yangli Che, Mingzhi Liu, Naiyu Zhang, Yang Zhou, Lihua Dong, Shen Li, Owen A. Sherwood, Min Yu, Zongheng Chen, Shengxiong Yang, Nan Wang, Longhai Zhu, Jiawang Chen, Mutai Bao, Haoshuai Li, Luonan Chen, Weifeng Wu, Haiyue Ma, David J. Burdige

OES Faculty Publications

Methane released from the subseafloor is significantly attenuated during upward migration, yet the preservation of methane-derived organic carbon (OC) in global deep-sea sediments remains poorly understood. Here, we measured carbon isotopes coupled with temperature-ramped analyses on various methane seepage sediments. Our results reveal a correlation between the radiocarbon (¹⁴)C) content in deep-sea surface sediments and sulfate-methane transition depth. Notably, our findings suggest that a substantial amount of (¹⁴)C-depleted OC may originate from deep-seated methane and is efficiently preserved in surface seepage sediments. We propose that the efficient OC preservation is related to microbial-mediated aggregate formation at the seawater-sediment interface, where …

The Effects Of A Microplate On Plume-Ridge Interactions: Constraints From Comparing Easter And Juan Fernandez Microplates In The Eastern Pacific Ocean, Katherine Ames, Jennifer Georgen

OES Faculty Publications

This study investigates the nature of plume-ridge interactions near a tectonic microplate using mantle Bouguer anomaly (MBA) gravity calculations. The focus of this investigation is a comparison of the Easter and Juan Fernandez microplates, which are located in the eastern Pacific Ocean along the Pacific, Nazca, and Antarctic plate boundaries. The microplates have several similar characteristics, including general size, time of formation, and clockwise rotation within the larger bounding mid-ocean ridge systems. Unlike the Juan Fernandez microplate, however, the Easter microplate is located near a mantle plume (Easter/Salas y Gomez). Previously published geochemical data suggest that material from this plume …

Differences In Sideerophore Production During The Growth Of Phytoplankton In Southern Ocean Incubation Experiments Under High- And Low-Iron Conditions, Randelle M. Bundy, Kristen N. Buck, Bethany D. Jenkins, P. Dreux Chappell, Daniel J. Repeta, Alexa Sterling, Shannon M. Yang, Laura Holland, Léo Mahieu, Laura E. Moore

OES Faculty Publications

Iron is an important micronutrient required by marine microorganisms. The Southern Ocean is an ecosystem where primary production is limited by the availability of iron, but how microorganisms in this region adapt to low-iron conditions or respond to episodic iron inputs is understudied. We tested how external iron additions would impact bacterial production of siderophores during phytoplankton growth using shipboard incubation experiments under a range of iron conditions. Similar heterotrophic bacteria communities and phytoplankton biomass were observed whether iron was added from the continental margin or as inorganic iron. Under both high- and low-iron conditions, the heterotrophic bacteria community remained …

Different Last Millennium El Niño Southern Oscillation Sea Surface Temperature Patterns Drive Disparate North Atlantic Tropical Cyclone Characteristics, Elizabeth Wallace, Sylvia Dee, Andrew Bierbower, Xinyue Luo, Richard Sullivan, Wenchang Yang, Gabe Vecchi, Kerry Emanuel

OES Faculty Publications

Understanding the relationship between the El Niño-Southern Oscillation (ENSO) phenomenon and North Atlantic tropical cyclone (TC) activity is critical for both seasonal predictions and future projections of TCs. Unfortunately, the satellite observational era (1970-present) captures too few El Niño events to fully characterize the response of TC activity to this multivariate, multi-scalar, and non-linear climate phenomenon. Here we explore ENSO-TC teleconnections using large data sets (>100 k) of synthetic North Atlantic tropical cyclones simulated for the past millennium using three different climate reconstructions - two earth system models (Max Planck Institute, Community Earth System Model) and one paleoclimate data …

Decoupling Of Dissolved Iron And Iron-Binding Humic-Like Substances Along The West Antarctic Peninsula, Laura E. Moore, Alayna Kisiday, Shannon M. Yang, P. Dreux Chappell, Randelle M. Bundy, Bethany D. Jenkins, Kristen N. Buck

OES Faculty Publications

The chemical speciation of iron (Fe) has important ramifications for the stabilization, transport, and bioavailability of this critical nutrient. Organic ligands mediate dissolved Fe biogeochemistry such that ligand concentration and molecular composition help shape dissolved Fe distributions. Electroactive Fe-binding humic-like substances ("humic substances") are one such class of ligands, a mixture thought to be predominantly comprised of degradation products of marine and terrestrial origin. Here, we examine the distributions of humic substances across large environmental gradients in dissolved Fe along the West Antarctic Peninsula in early austral spring. We found that the distributions of humic substances and dissolved Fe were …

Likelihood-Based Inference For Random Networks With Changepoints, Daniel Cirkovic, Tiandong Wang, Xianyang Zhang

Mathematical and Statistical Science Faculty Research and Publications

Generative, temporal network models play an important role in analyzing the dependence structure and evolution patterns of complex networks. Due to the complicated nature of real network data, it is often naive to assume that the underlying data-generative mechanism itself is invariant with time. Such observation leads to the study of changepoints or sudden shifts in the distributional structure of the evolving network. In this paper, we propose a likelihood-based methodology to detect changepoints in undirected, affine preferential attachment networks where, upon introduction, a new node selects one old to attach to with probability proportional to its degree. In particular, …

Symmetry In Latin Hypercubes, Levi Neiburger

Theses and Dissertations

Let [n] = {1, ..., n}. A hypercube H of order n and dimension d is a d-dimensional array whose nᵈ cells are indexed by [n]ᵈ. A hyperplane in H is obtained by fixing one coordinate, while allowing the remaining d–1 coordinates to vary. We wish to color each cell of H from a palette of n^d-1 colors such that each hyperplane is polychromatic.

Our main result is the following. Let n be sufficiently large. There exists a symmetric coloring of the d-dimensional hypercubes of order n whose all hyperplanes are polychromatic if and only if: …

Investigating Phosphorus Load Trends And Driving Factors In Illinois Watersheds Using Machine Learning Algorithms, Hannah Lartey

Theses and Dissertations

Phosphorus (P) pollution in Illinois watersheds has become a significant water quality concern. Recent studies have shown increasing concentrations in streams and rivers, leading to eutrophication, which damages aquatic ecosystems and threatens human health. This study examines temporal trends in total phosphorus loads across 79 monitoring stations in Illinois from 1979 to 2020 and identifies the main environmental factors that influence P load variability. Trend analyses were conducted using the nonparametric Mann-Kendall and Sen’s slope methods. GIS-based climate, hydrology, and soil property datasets were assembled for each monitoring station. These datasets were used to build machine learning models using the …

Theoretical Analysis Of Filtering And Smoothing Techniques In Stochastic Time Series, Kaosarat Bola Azeez

Theses and Dissertations

Polynomial-preserving linear filters are fundamental tools for smoothing and trend extraction in noisy time series, particularly when the objective is to reduce short-run variation without distorting underlying low-degree structure. This thesis develops a general framework for such filters based on local polynomial approximation and least-squares estimation. In particular, we establish that the resulting estimators can be represented as symmetric linear filters whose weights satisfy moment conditions that ensure exact polynomial reproduction up to a specified degree. Building on this framework, we derive explicit coefficient vectors for several classical smoothing filters, including the Savitzky-Golay filters SG(5,2) and SG(7,3), as well as …

An Application Of Molecular Dynamics To Hed Plasma Physics: Point And Group Defect Diffusion In Coulomb Crystals, Levi Webb

Theses and Dissertations

Molecular dynamics (MD) simulations are used to explore the microscopic behaviors of complex systems that cannot be easily studied experimentally. In particular, the microphysics of high energy density (HED) astrophysical plasma environments remain inaccessible by modern experiment---even in laser facilities, these plasmas exist only on short timescales that do not lend easily to investigation. The diffusion of point and group defects through crystallized plasmas in the cores of white dwarfs and neutron star crusts, called Coulomb crystals, has potentially macroscopic implications for the evolution of these bodies. Thus, I employ the widely-used MD code LAMMPS to simulate small Coulomb crystal …

How And Why Preservice Mathematics Teachers’ Respond To Students’ Statistical Thinking, Radhika Pathak Kharel

Theses and Dissertations

Researchers have found that how preservice teachers (PSTs) respond to students' thinking is crucial to their students' learning and to PSTs' own teaching effectiveness. Although there are some research studies on how teachers respond, there is relatively scarce research on why PSTs respond to students’ thinking the way they do. Such understanding is crucial for designing mathematics methods courses and other professional development opportunities that enable PSTs to create more thoughtful and effective teaching plans. I examined how and why PSTs respond in-the-moment to students’ statistical thinking. The study involved 16 PSTs who enrolled in a middle school mathematics methods …

Fostering A Growth Mindset In Mathematics: Faculty And Student Experiences, Yolanda G. Rush

Theses and Dissertations

According to the Center for Community College Student Engagement (2019), many students attending two-year institutions need productive persistence strategies, including the development of a growth mindset. Although some growth mindset interventions have been effective in improving academic achievement among students (Boaler, 2016; Canning et al., 2024) and persistence (Lewis, 2019) among students, especially those with developmental needs (Suh et al., 2019) and those in mathematics, little is known about the experiences of students and teachers (i.e., students’ perceptions of teachers’ intentions and implementation) as teachers work to foster a growth mindset culture (Murphy et al., 2021). In this dissertation, I …

High-Resolution Mapping Of Soil Moisture Variation Using Uas Thermal And Multispectral Imagery, Jackline Amma Timah

Theses and Dissertations

In agricultural landscapes, soil moisture regulates hydrologic partitioning, nutrient transport and water quality, land-atmosphere energy exchange that shapes local climate, and ecosystem resilience. However, traditional monitoring approaches, such as in-situ sensors and satellite imagery, often lack the spatial resolution required to capture fine-scale soil moisture variability. This study evaluated whether unmanned aerial system (UAS)-derived thermal, multispectral, and terrain variables can capture fine-scale spatial variability in volumetric water content (VWC) within an SRB in central Illinois.

High-resolution imagery was collected and paired with 50 field-measured VWC observations. Land surface temperature (LST), vegetation indices (NDVI and NDRE), spectral bands, and slope were …

Type Ii Diabetes Treatment Comparison Via Compartment Modeling, Abigail M. Collins

Theses and Dissertations

Type II diabetes mellitus affects one in ten adults worldwide, yet the effects of treatment type and adherence level on developing complications and quality of life have not been well characterized at the population level, and mathematical modeling offers a structured way to examine these dynamics. This thesis adapts the Boutayeb et al. (2004) model to incorporate dynamic treatment types and levels of adherence, producing nine scenarios in which complication development rate and complication recovery rate differed, to compare peak complications and quality of life across treatment and adherence conditions. Using a system of ordinary differential equations and compartment modeling, …

Managing Multi-Drug Resistance: An Evolutionary Game Theory And Optimal Control Approach, Shukhrat Nasrulloev

Theses and Dissertations

Multi-drug resistance is an evolutionary process in which treatment eliminates sensitive cells, allowing resistant clones to dominate. This thesis investigates this process using a framework integrating population dynamics, evolutionary game theory, and optimal control theory. We develop a two-population logistic growth model describing competition between drug-sensitive and drug-resistant cells under treatment, construct dose-dependent payoff matrices and replicator dynamics to characterize evolutionary competition, and derive a critical drug level D_crit = (r_S - rR)/(dS - d_R) at which resistant cells gain a fitness advantage. An optimal control problem is formulated via Pontryagin's Maximum Principle to identify schedules …

Data Defines Success: Algorithm For Dataset Quality Assessment In Deep Learning For Malware Detection, Matei Ionescu

Theses and Dissertations

The field of artificial intelligence is based upon the premise of constructing architectures through which to propagate training data. However, the majority of existing research literature is focused on architecture. While necessary, the attention devoted to the architecture should not so precipitously exceed that of the data. It should be noted that this disparity is not without reasonable cause. Data quality is often exceedingly difficult to verify due to particularities of the field or subfield; LLM repositories of text are distinct from image recognition pictures of dog breeds which are distinct from EEG waveforms of human brains which are distinct …

Training Set Augmentation And Biology-Aware Harmonization Improve Radiomic Models For Lung Cancer Prediction In Indeterminate Nodules, Claire Huchthausen, Menglin Shi, Gabriel De Sousa, James Larner, Einsley Janowski, Jonathan Colen, Krishni Wijesooriya

Data Science Faculty Publications

CT radiomics-based machine learning has potential to predict lung cancer in pulmonary nodules (PNs) earlier than standard-of-care methods. Low malignancy rates in early-development PNs and variable image acquisition hinder development of radiomic models for diagnosing these PNs. To address these challenges, we augmented training using later-development PNs and harmonized for acquisition effects. We examine early-development benign and malignant PNs (n = 106) below the sensitivity of standard-of-care diagnosis. Classifiers predicting malignancy performed near chance when trained on ComBat-harmonized radiomic features from only early-development PNs. We then augmented training with later-development benign and malignant PNs (n = 225). We evaluated whether …

Applied Machine Learning In Mineral Prospectivity Mapping In The South Pass-Granite Mountains Of Wyoming, Carl D. York

Graduate Theses/Dissertations

The South Pass-Granite Mountains, comprised of Archean to Tertiary rocks embedded with an Archean greenstone belt in Central Wyoming, have historically been mined for gold, iron, steel, and silver. Rare earth elements have been of increasing interest in the region and thus, several datasets have become available. Knowledge driven and data driven models are used in mineral prospectivity mapping with input data including geological mapping, geochemical data, geophysical (USGS Critical Mineral magnetic and gravity data), radiometric (U, Th, K) data and multispectral remote sensing data. Mineral prospectivity has seen a rapid improvement in recent years using advancements in machine learning …

Knowing The User: Representation, Contextualization, And Predictive Internalization In Personalized Models, Zhongyu Ouyang

Dartmouth College Ph.D Dissertations

Intelligent systems increasingly anticipate which items a person will prefer, adapt generated text to a familiar style, and carry relevant information across interactions. These capabilities invite the impression that a model knows its user. In the technical sense studied here, a model knows a user when it carries information specific to that user, uses that information in the relevant context, and generalizes beyond the observations used to build the user state. Knowing is thus a measurable relation among user evidence, model state, context, and held-out user-specific behavior. The research community generally studies this family of systems under the term personalization, …

Advancing Periodic Time Series Analysis: Application, Bias Assessment, And Optimal Window Selection In The Variable Bandpass Periodic Block Bootstrap Method, Yanan Sun

Electronic Theses & Dissertations (2024 - present)

Time series analysis is essential for understanding long-term patterns, periodic behavior, and underlying correlations in complex datasets. The periodically correlated (PC) time series is a type of time series where the correlation structure repeats over fixed intervals. The Variable Bandpass Periodic Block Bootstrap (VBPBB) has recently been proposed as a resampling method that preserves PC structures through the use of periodogram, bandpass filters, and block bootstrap resampling. Although promising, VBPBB remains underutilized, and its limitations have not been fully examined. This dissertation advances both the application and methodological development of the VBPBB.

The first project applies the VBPBB to a …

The Maxima Method For Identification Of Principal Periodic Components In Time Series Analysis, Megan Di Maio

Electronic Theses & Dissertations (2024 - present)

This dissertation investigates methods for mean estimation in periodically correlated time series, focusing on the Variable Bandpass Periodic Block Bootstrap (VBPBB) and a novel data-driven maxima method. Time series require specific methods because of the temporal correlation in the data. Traditional methods like the General Seasonal Block Bootstrap (GSBB) account for this correlation but often produce wide confidence intervals because they cannot isolate multiple periodicities, allowing noise and other frequencies to interfere with analysis. The VBPBB method addresses this by applying a Kolmogorov-Zurbenko Fourier Transform (KZFT) filter to the data before bootstrapping, which suppresses interfering frequencies and results in narrower, …

Medical Linear Accelerator Water Tank Measurements Optimization For Commissioning, Tyler R. Laugh

Theses and Dissertations

Beam commissioning is a critical component of linear accelerator (LINAC) implementation, requiring accurate measurement of percent depth dose (PDD), beam profiles, and output factors across a wide range of field sizes. Conventional commissioning workflows often require multiple detectors and can be time-intensive, particularly for small-field dosimetry where measurement accuracy is highly sensitive to detector characteristics. This study evaluated the performance of a plastic scintillation detector (BP-PSD) for full water tank commissioning and its potential to improve efficiency while maintaining dosimetric accuracy.

Beam data were acquired for field sizes ranging from 1 × 1 cm² to 40 × 40 cm² using …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

A Mathematical Frameworks For Singular, Nonlinear Phenomena: Applications To Nematocyst Firing And Inhomogeneous Nls With Coulomb Potential, Abdulrahman Alharbi

Theses and Dissertations

Nematocysts are specialized cellular organelles found in all cnidarians, including corals and jellyfish, as well as in some single-celled protists such as dinoflagellates. These organelles display remarkable diversity in morphology and function, playing roles in prey capture and defense. The firing of a nematocyst is one of the fastest accelerations in nature, yet the underlying physical mechanisms remain not fully understood. In this work, we address key questions: how sufficient force is generated to overcome the fluid boundary layer, whether fluid–structure interaction models can reproduce observed dynamics, and what mechanisms trigger discharge.

Our research investigates models based on osmotic pressure …

Untrained Position-Encoded Multilayer Perceptron Network For Structured Illumination Microscopy Reconstruction, Sahil Sharma, Leonidas Zimianitis, Krishnendu Samanta, Balpreet Singh Ahluwalia, Joby Joseph, Dushan N. Wadduwage

Computer Science Faculty Publications

Structured Illumination Microscopy (SIM) enables super-resolution imaging by encoding high-frequency spatial information through patterned light. While traditional Fourier-based reconstruction methods are prone to artifacts under suboptimal conditions, recent deep learning approaches often require large training datasets and lack adaptability across different imaging setups. In this work, we present Position Encoded Multi-Layer Perceptron (PEM) network that leverages implicit neural representations (INRs) and SIM forward-model-driven modeling to reconstruct super-resolved images without any training data. PEM-SIM represents each spatial coordinate as a combination of sinusoidal functions across multiple frequencies, enabling rich encoding of fine spatial detail. A forward model grounded in SIM image …

Sage: Spatially Aware Gene Selection And Dual-View Embedding Fusion For Domain Identification In Spatial Transcriptomics, Yi He, Yunpei Xu, Liqing Ding, Hong-Dong Li, Yaohang Li, Shaokai Wang

Computer Science Faculty Publications

Despite enabling high-resolution mapping of gene expression within tissues, spatial transcriptomics (ST) still faces challenges in accurately segmenting spatial domains due to complex tissue architecture and limitations of current methods. Most approaches rely on local spatial priors, lack gene-level interpretability, and fall short in capturing structure-discriminative genes or long-range functional relationships, limiting their ability to resolve biologically meaningful architectures. We present Spatially Aware Gene selection and dual-view Embedding fusion (SAGE), a unified and reproducible framework for domain identification in spatial transcriptomics that combines topic-driven gene selection with dual-view embedding fusion to address these gaps. SAGE integrates non-negative matrix factorization (NMF)-based …

Design And Analysis Of Modern Quantum Neural Network Architectures For Intelligent Systems, Lakshmi Chandrakanth Kasireddy, Prabhakara Rao Kapula, Dineshkumar Rajendran, Neha Bharani, Srikanth Pulipeti, Islombek Khushvaktov

Computer Science Faculty Publications

Quantum neural networks (QNNs) offer a principled pathway for integrating quantum computation with machine learning through superposition- and entanglement-based representations. This chapter proposes an architecture-aware design and evaluation framework for modern QNNs, emphasizing robustness and system feasibility alongside predictive performance. Multiple architectures variational QNNs, quantum convolutional neural networks, tensor-network hybrids, and fully quantum models—are assessed under a unified protocol. Experimental analysis shows that the proposed architecture-search–guided QNN achieves 91.8% classification accuracy and an F1-score of 0.914, outperforming fixed-template variational QNNs by approximately 5.6 percentage points. Under depolarizing noise with probability p = 0.10, the proposed model retains 85.3% accuracy, whereas …

Integration Of Hybrid Quantum-Neuromorphic Ai With Cloud, Edge, And High-Performance Computing Environments, Arun B. Prasad, Ajay Prasad, Dineshkumar Rajendran, Anurag Tiwari, T. Akilan, Islombek Khushvaktov

Computer Science Faculty Publications

The convergence of quantum computing, neuromorphic learning, and distributed cloud infrastructures has occurred very rapidly, and intelligent systems are now providing new opportunities, but the challenge of instability, complexity of orchestration, and noise sensitivity remains in the way of practical integration. The proposed work is based on a hybrid quantum and neuromorphic architecture, which is the integration of event-based neuromorphic adaptation and quantum-assisted global optimization, orchestrated by cloud-HPC. The architecture presents the thermodynamically regularized learning and resourceful task scheduling to the probabilistic search and the continuous local adaptation. Experimental evaluation across financial modeling, medical imaging, and physical system prediction shows …

Quantum Machine Learning Models: Principles, Frameworks, And Computational Challenges, K. A. Jayabalaji, S. Venkata Anand, Dineshkumar Rajendran, Prasanta Chatterjee Biswas, Sardor Omonov, Rubaid Ashfaq

Computer Science Faculty Publications

Quantum machine learning (QML) has become an optimistic avenue of harnessing quantum computation in data-driven modeling, especially of issues with high dimensionality and complicated correlations. Current methods are generally based on fixed or over-parameterized quantum circuits, and hence restricted to scalability as well as unproductive optimization in real-world hardware. This chapter introduces a hybrid quantum-classical learning system that is adaptive and provides principled quantum data encoding, architecture-conscious variational circuit design and resource-optimal optimization. The technique is based on the concepts of quantum architecture search and subspace-preserving transformations to trade expressiveness with trainability, and discretize the quantum model into a classical …

Contextual Scaffolding And Self-Efficacy: Supporting Computer Skill Development Among Blind Learners In India, Akshay Kolgar Nayak, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Inclusive computer literacy education efforts, broadening the participation of blind or visually impaired (BVI) individuals, have gained traction in recent years. Existing literature investigating these efforts primarily draws evidence from affluent Global North contexts, where accessibility resources and legal frameworks are relatively more mature. Little is known about the in-situ teaching and learning challenges faced by trainers and BVI students, respectively, in resource-constrained, multicultural Global South countries like India. To address this knowledge gap, we conducted a four-month contextual inquiry at two computer training centers catering to 94 BVI students in India. We notably observed a rigid, experience-driven training environment …